Merge pull request #32 from Herculens/pr-versioning

Add proper versioning

.github/workflows/publish-to-pypi.yml

@@ -0,0 +1,25 @@
+name: Publish to PyPi
+
+on: workflow_dispatch
+
+jobs:
+  build-and-publish:
+    name: Build python package and publish to PyPi
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@master
+    - name: Set up Python 3.11
+      uses: actions/setup-python@v2
+      with:
+        python-version: 3.11
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install setuptools wheel
+    - name: Build
+      run: python setup.py sdist bdist_wheel
+    - name: Publish to PyPi
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        user: __token__
+        password: ${{ secrets.PYPI_API_TOKEN }}

.github/workflows/publish-to-testpypi.yml

@@ -0,0 +1,26 @@
+name: Publish to Test PyPi
+
+on: workflow_dispatch
+
+jobs:
+  build-and-publish:
+    name: Build python package and publish to Test PyPi
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@master
+    - name: Set up Python 3.11
+      uses: actions/setup-python@v2
+      with:
+        python-version: 3.11
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install setuptools wheel
+    - name: Build
+      run: python setup.py sdist bdist_wheel
+    - name: Publish to Test PyPi
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        user: __token__
+        password: ${{ secrets.TEST_PYPI_API_TOKEN }}
+        repository_url: https://test.pypi.org/legacy/

README.md

@@ -1,4 +1,5 @@
-<img src="images/horizontal.png" width="600" alt="Herculens logo" />
+<img src="https://raw.githubusercontent.com/Herculens/herculens/main/images/horizontal.png#gh-light-mode-only" width="600" alt="Herculens logo" />
+<img src="https://raw.githubusercontent.com/Herculens/herculens/main/images/horizontal_dark_bg.png#gh-dark-mode-only" width="600" alt="Herculens logo" />
 
 # Herculens: differentiable gravitational lensing
 

herculens/__init__.py

@@ -1,4 +1,19 @@
-__author__ = 'Austin Peel, Aymeric Galan, Giorgos Vernardos and contributors'
+"""
+
+This file initializes the coolest module
+and provides some basic information about the package.
+
+"""
+
+# Set the package release version
+version_info = (0, 0, 1)
+__version__ = '.'.join(str(c) for c in version_info)
+
+# Set the package details
+__author__ = 'Aymeric Galan, Austin Peel, Giorgos Vernardos & Herculens contributors'
 __email__ = '[email protected]'
-__version__ = '0.0.1'
-__credits__ = 'EPFL'
+__year__ = '2021-2024'
+__credits__ = 'Herculens contributors, EPFL (see AUTHORS.md)'
+__url__ = 'https://github.com/austinpeel/herculens'
+__description__ = 'Auto-differentiable strong lens modelling'
+__license__ = 'MIT'

requirements.txt

@@ -2,16 +2,15 @@ numpy>=1.20.3
 scipy>=1.6.3
 jax>=0.3.14
 jaxlib>=0.3.14
-optax>=0.1.0
-jaxopt>=0.5.5
-chex>=0.1.4
 objax>=1.7.0
-matplotlib>=3.0.0
-findiff==0.8.9
 scikit-image>=0.20.0
 git+https://github.com/aymgal/utax.git@main#egg=utax   # JAX utilities (convolution, interpolation, etc.)
 
 # the following packages are optional (pay attention to the versions)
+#optax>=0.1.0        # for optimizers
+#jaxopt>=0.5.5       # for optimizers
+#matplotlib>=3.7.0   # for plotting
+#findiff==0.8.9      # for building matrix with finite difference coefficients
 #tqdm>=4.61.0        # for progress bars with certain optimizers and samplers
 #numpyro==0.10.1     # for SVI and HMC sampling
 #blackjax==0.9.6     # for JAX-based HMC sampling

setup.py

@@ -1,31 +1,67 @@
 import setuptools
 import os
 
-__name__ = 'herculens'
+name = 'herculens'
 
 release_info = {}
 infopath = os.path.abspath(os.path.join(os.path.dirname(__file__),
-                           __name__, 'info.py'))
+                           name, '__init__.py'))
 with open(infopath) as open_file:
     exec(open_file.read(), release_info)
 
 this_directory = os.path.abspath(os.path.dirname(__file__))
 with open(os.path.join(this_directory, 'README.md'), encoding='utf-8') as f:
-    long_description = f.read()
+    readme = f.read()
+
+# Use the README as long description but remove the second version 
+# of the logo (readable only by GitHub's dark mode interface)
+long_description = readme.replace('<img src="https://raw.githubusercontent.com/Herculens/herculens/main/images/horizontal_dark_bg.png#gh-dark-mode-only" width="600" alt="Herculens logo" />', '')
+
+# Python version
+python_requires = '>=3.8'
+
+# Minimal required packages (see requirements.txt for versions)
+install_requires = [
+    'numpy',
+    'scipy',
+    'jax',
+    'jaxlib',
+    'objax',
+    'scikit-image',
+    # 'https://github.com/aymgal/utax.git',  # use requirements.txt
+]
+
+# Minimal optional packages (see requirements.txt for versions and complete list)
+install_optional = [
+    'matplotlib',    # for plotting
+    'optax',         # for optimizers
+    'jaxopt',        # for optimizers
+    'findiff',       # for building matrix with finite difference coefficients
+    'numpyro',       # for SVI and HMC sampling
+    'blackjax',      # for JAX-based HMC sampling
+]
+
+version = release_info['__version__']
 
 setuptools.setup(
-    name=__name__,
+    name=name,
     author=release_info['__author__'],
     author_email=release_info['__email__'],
-    version=release_info['__version__'],
+    version=version,
     url=release_info['__url__'],
+    download_url=f"https://github.com/Herculens/herculens/archive/refs/tags/v{version}.tar.gz",
     packages=setuptools.find_packages(),
-    python_requires=release_info['__python__'],
-    install_requires=release_info['__requires__'],
     license=release_info['__license__'],
-    description=release_info['__about__'],
+    description=release_info['__description__'],
     long_description=long_description,
     long_description_content_type='text/markdown',
-    setup_requires=release_info['__setup_requires__'],
-    tests_require=release_info['__tests_require__']
+    keywords=["herculens", "lensing", "gravitation", "astrophysics"],
+
+    python_requires=python_requires,
+    install_requires=install_requires,
+    extras_require={
+        "opt": install_optional,  # installable via `pip install herculens[opt]`
+    },
+    setup_requires=['pytest-runner',],
+    tests_require=['pytest', 'pytest-cov', 'pytest-pep8'],
 )

test_requirements.txt

@@ -1,4 +1,7 @@
 tqdm>=4.61.0        # for progress bars with certain optimizers and samplers
 numpyro>=0.10.1     # for SVI and HMC sampling
+optax>=0.1.0        # for optimizers
+jaxopt>=0.5.5       # for optimizers
+matplotlib>=3.7.0   # for plotting
 git+https://github.com/adam-coogan/jaxinterp2d@9881075#egg=jaxinterp2d  # for fast bilinear interpolation (e.g. for pixelated profiles)
 git+https://github.com/Herculens/helens.git@main#egg=helens  # lens equation solver